9CNZ: BAM

Structure of BAM complexed with PTB2 ligand in detergent. Determined by electron microscopy at 3.1 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Escherichia coli, synthetic construct
Chains: 8
Atoms: 12,854
Mol. weight: 216.88 kDa
Released: 25 Dec 2024

Explore 9CNZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CNZ contains 55 α-helices and 110 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	28-32	5	2
α-helix	39-45	7
β-strand	53	1	1
α-helix	56-67	12
β-strand	72-80	9	2
β-strand	83-90	8	2
β-strand	92	1	3
β-strand	94-100	7	4
α-helix	108-117	10
β-strand	124	1	3
α-helix	127-129	3
α-helix	130-143	14
β-strand	150-155	6	4
β-strand	163-170	8	4
α-helix	171-175	5
β-strand	176-183	8	5
α-helix	190-194	5
α-helix	205-207	3
β-strand	213	1	5
α-helix	216-232	17
β-strand	239-247	9	5
β-strand	253-261	9	5
β-strand	267-276	10	6
α-helix	281-287	7
α-helix	294	1
β-strand	295	1	6
α-helix	296	1
α-helix	298-313	16
β-strand	321-329	9	6
β-strand	334-342	9	6
β-strand	348-355	8	7
α-helix	362-366	5
β-strand	375-376	2	7
α-helix	379-392	14
β-strand	395-404	10	7
α-helix	405	1
β-strand	411-420	10	7
β-strand	425-434	10	8
β-strand	437-446	10	8
α-helix	449-451	3
β-strand	455-462	8	8
β-strand	466-475	10	8
β-strand	484-495	12	8
β-strand	505-518	14	8
β-strand	523-537	15	8
α-helix	539-541	3
β-strand	542	1	9
α-helix	543-551	9
β-strand	560	1	10
β-strand	564-579	16	8
β-strand	590-600	11	8
α-helix	601	1
β-strand	608-620	13	8
β-strand	628-640	13	8
α-helix	648-650	3
β-strand	652	1	11
β-strand	654	1	12
β-strand	663	1	13
β-strand	668	1	12
β-strand	671-674	4	9
β-strand	677	1	14
β-strand	678	1	10
β-strand	691	1	14
β-strand	700-705	6	9
β-strand	708	1	11
β-strand	710-720	11	8
α-helix	730-732	3
β-strand	733-745	13	8
β-strand	767-778	12	8
β-strand	781-792	12	8
α-helix	797-798	2
β-strand	799	1	13
β-strand	802-806	5	8

Chain B: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	31-36	6
β-strand	46-51	6	15
β-strand	66-68	3	16
β-strand	71-75	5	16
β-strand	80-85	6	16
β-strand	91-96	6	16
α-helix	114-115	2
β-strand	116-118	3	17
β-strand	121-126	6	17
β-strand	130-135	6	17
β-strand	141-146	6	17
β-strand	151	1	18
α-helix	154-155	2
β-strand	156-158	3	19
β-strand	161-165	5	19
β-strand	166	1	18
β-strand	171-175	5	19
β-strand	181-185	5	19
β-strand	193-194	2	5
α-helix	198-200	3
β-strand	201-203	3	20
β-strand	206-210	5	20
β-strand	215-220	6	20
β-strand	226-231	6	20
β-strand	248	1	21
β-strand	252-254	3	22
β-strand	257-261	5	22
β-strand	262	1	21
β-strand	267-271	5	22
β-strand	277-281	5	22
β-strand	290-292	3	23
β-strand	295-299	5	23
β-strand	305-309	5	23
β-strand	315-319	5	23
β-strand	327	1	24
α-helix	328-330	3
β-strand	331-333	3	25
β-strand	336-340	5	25
β-strand	341	1	24
β-strand	345-350	6	25
β-strand	356-361	6	25
α-helix	370-371	2
β-strand	372-374	3	15
β-strand	377-381	5	15
β-strand	386-390	5	15

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	44-47	4
α-helix	49-53	5
α-helix	58-62	5
α-helix	63-65	3
α-helix	77-79	3
α-helix	84-86	3
β-strand	99-100	2	26
β-strand	103-104	2	26
β-strand	107-109	3	27
α-helix	116-126	11
β-strand	157-163	7	26
β-strand	166-168	3	27
β-strand	171-173	3	27
β-strand	176-183	8	26
β-strand	186-188	3	26
α-helix	191-210	20

Chain D: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	27-29	3
α-helix	32-44	13
α-helix	48-61	14
α-helix	68-81	14
α-helix	85-98	14
α-helix	105-119	15
α-helix	123-127	5
α-helix	132-134	3
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	209-224	16
α-helix	228-240	13

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	28
α-helix	40-43	4
β-strand	51	1	29
α-helix	52-59	8
β-strand	64-65	2	28
β-strand	72-80	9	28
β-strand	87-95	9	28
β-strand	100	1	29
β-strand	101-107	7	28

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	8
α-helix	6-8	3

Chain H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	8
β-strand	8-13	6	8

Chain I: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	30
α-helix	5-7	3
β-strand	9-11	3	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	810	Escherichia coli	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	392	Escherichia coli	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	344	Escherichia coli	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	245	Escherichia coli	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	123	Escherichia coli	P0A937
PTB2 circular peptide	G, H, I	protein	17	synthetic construct

Sequence of entity 1 (A), FASTA

>9CNZ_1 Outer membrane protein assembly factor BamA (chains A)
MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDIS
NTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVR
VGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQI
NIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNI
DSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTK
VTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTS
KDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKE
RNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV
DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQ
PQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVT
IPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTV
RGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFIT
PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPL
GPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (B), FASTA

>9CNZ_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITR

Sequence of entity 3 (C), FASTA

>9CNZ_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>9CNZ_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>9CNZ_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHH
HHH

Sequence of entity 6 (G, H, I), FASTA

>9CNZ_6 PTB2 circular peptide (chains G, H, I)
XFGTIHKRRFRYWFCGX

Primary citation

The discovery and structural basis of two distinct state-dependent inhibitors of BamA. Sun, D., Storek, K.M., Tegunov, D. et al. Nat Commun (2024) 15:8718-8718. DOI 10.1038/s41467-024-52512-1 · PubMed

Other PDB entries of the same protein (UniProt P0A940 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3Q6B 1.5 Å, The high-resolution and new form crystal structure of BamA POTRA4-5 from E.coli
9CS2 1.78 Å, E. coli BamA beta-barrel bound to cyclic peptide CP3
6QGW 1.94 Å, Crystal structure of E.coli BamA beta-barrel in complex with nanobody E6
9CS0 1.94 Å, E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP1
9CS1 2.15 Å, E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2
4XGA 2.15 Å, Crystal structure of BamB and BamA P3-5 complex from E.coli
2QDF 2.2 Å, Structure of N-terminal domain of E. Coli YaeT
6QGX 2.2 Å, Crystal structure of E.coli BamA beta-barrel in complex with nanobody F7
7NRF 2.2 Å, Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)
7NRE 2.3 Å, Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1)
7P1C 2.5 Å, Crystal structure of E.coli BamA beta-barrel in complex with darobactin B
7R1V 2.5 Å, Crystal structure of E.coli BamA beta-barrel in complex with dynobactin A

Browse structure collections

About this viewer

MolViewer shows 9CNZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.